PHASEBOOK is an haplotyping programs package: LinkPHASE,HiddenPHASE, DualPHASE and DAGPHASE. The proposed methods work in two steps. First, haplotypes are reconstructed based on familial information (Mendelian segregation rules and linkage information) and next it fills in the gaps by applying a Hidden Markov Model (models from fastPHASE (Scheet and Stephens, 2006) or from Beagle (Browning and Browning, 2007)).
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LINKPHASE3: an improved pedigree-based phasing algorithm robust to genotyping and map errors.
Druet T, Georges M.
Bioinformatics. 2015 Jan 7. pii: btu859.
Druet & Georges, 2010
A Hidden Markov Model Combining Linkage and Linkage Disequilibrium Information for Haplotype Reconstruction and Quantitative Trait Locus Fine Mapping
Genetics. 2010 Mar;184(3):789-98.